Hen-egg problem: did RNA or proteins come first: or was it pre-tRNA?

The notions of magnetic body, dark matter as h_eff=nh₀ phases, dark analogs of information molecules, and resonance mechanism could allow a solution to the hen-egg-problem of biology: which came first, DNA, RNA, or AAs.

Hen-egg problem usually means that something is missing from the conceptual picture and TGD based quantum biology suggests what this missing piece could be. The general solution of the problem in TGD would be that dark analogs of information molecules emerged first simultaneously as Galois confined states of dark proton-triplets and dark photon-triplets.

This made possible resonance communications and the basic recognition mechanism by 3-resonance for dark 3-photons. DX-X pairing was based on energy resonance and these composites were able to find each other by resonance. The reduction of h_eff for connecting flux tubes in their shortening liberated energy making it possible to overcome the potential wall preventing chemical reactions to occur.

The challenge is to develop a more detailed picture around these basic ideas. The popular article telling about work telling about the formation of analogs of sequences of DNA analogs of tRNA (this) led to a proposal about first steps of the evolution of basic bio-molecules. I have earlier considered several proposals of this kind but without the recent view about resonance mechanism (see this,this and this).

The experimenters used analogs of tRNA formed from DNA codons and amino-acids attached to the tRNA-analogs. These tRNA-AA pairs consisting of 4 units could replicate. The geometry of tRNA analogs resembled the crux like geometry of tRNA and contained also the analog of RNA codon. The structure corresponds to 4 bits, which correspond to the first 2 letters of the genetic codon.

1. In a good approximation, the third letter of the genetic codon corresponds to a single rather than 2 bits. I have considered the possibility that the 3-letter code was formed as a product of 2-letter code and 1-letter code with A-T and C-G symmetries.
2. Could the wobble letter of tRNA codon, which corresponds to the third letter of RNA codon have interpretation as a letter, which originally coded for a single bit? This would mean 5 bit code. DtRNA indeed defines 5-bit code and 32 DtRNAs are the minimal option.

The codon part of tRNA is inside the anti-codon loop (see this).This does not provide obvious support for this view. For pre-tRNA involving only the codon part of tRNA the situation would have been different. Also an AA dominated era has been proposed and this option can be considered also from the TGD point of view. Enzymes are necessary for DNA replication, translation and transcription. Could proteins have served as the egg in the chemical sense in the TGD framework. Could the resonance mechanism together with the TGD view about bio-catalysis make it possible to generate proteins from DX-X pairs, where X is shorthand for AA–pre-tRNA pair? Suppose that pre-tRNA corresponds to the codon part of the recent tRNA. 6-bit genetic code would have evolved from 4-bit code, which indeed looks natural from the information theoretic perspective.

1. Resonance mechanism would make possible DX=DAA-DtRNA, DAA-AA and DtRNA–pre-tRNA pairings. Resonance could also give rise to primitive analogs of pre-tRNA-AA pairs. The energy liberated in the reduction of the flux tube length accompanying the reduction of h_eff could have made possible catalysis allowing overcome the potential wall for the formation of the valence (esther) bond between pre-tRNA and AA. Genetic code would be 5-bit code determined by the codon part of DtRNA and have exact A-U and G-C symmetries.

The generation of proteins could in turn catalyze the formation of DNA and RNA sequences and this would have opened the floodgates leading to the recent machineries of transcription and translation. The evolution of the ribosome machinery would have added additional parts to pre-tRNA necessary for the translation process and led to the recent tRNA.

One can also consider a variant of this option. The same process could lead to a transformation of AA-pre-tRNA ester bond to RNA-RNA valence bond and liberate AA. This option would resemble the RNA world. One can even consider the possibility that, depending on context, RNA sequences or AA sequences are formed. See the article Molecular Signalling from the TGD Point of View or the chapter with the same title.

For a summary of earlier postings see Latest progress in TGD.

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